An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots
Copyright 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1295-1304, 2004
| Veröffentlicht in: | Journal of computational chemistry. - 1984. - 25(2004), 10 vom: 30. Juli, Seite 1295-304 |
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| Format: | Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2004
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| Zugriff auf das übergeordnete Werk: | Journal of computational chemistry |
| Schlagworte: | Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. telomerase RNA RNA 63231-63-0 DNA 9007-49-2 Telomerase EC 2.7.7.49 |
| Zusammenfassung: | Copyright 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1295-1304, 2004 Given a nucleic acid sequence, a recent algorithm allows the calculation of the partition function over secondary structure space including a class of physically relevant pseudoknots. Here, we present a method for computing base-pairing probabilities starting from the output of this partition function algorithm. The approach relies on the calculation of recursion probabilities that are computed by backtracking through the partition function algorithm, applying a particular transformation at each step. This transformation is applicable to any partition function algorithm that follows the same basic dynamic programming paradigm. Base-pairing probabilities are useful for analyzing the equilibrium ensemble properties of natural and engineered nucleic acids, as demonstrated for a human telomerase RNA and a synthetic DNA nanostructure |
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| Beschreibung: | Date Completed 22.07.2004 Date Revised 15.11.2006 published: Print Citation Status MEDLINE |
| ISSN: | 1096-987X |